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Furtado CLM, da Silva Santos R, Sales SLA, Teixeira LPR, Pessoa CDÓ. Long Non-coding RNAs and CRISPR-Cas Edition in Tumorigenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1429:41-58. [PMID: 37486515 DOI: 10.1007/978-3-031-33325-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Long non-coding RNAs (lncRNAs) are one of the most abundant and heterogeneous transcripts with key roles in chromatin remodeling and gene regulation at the transcriptional and post-transcriptional levels. Due to their role in cell growth and differentiation, lncRNAs have emerged as an important biomarker in cancer diagnosis, prognosis, and targeted treatment. Recent studies have focused on elucidating lncRNA function during malignant transformation, tumor progression and drug resistance. The advent of the CRISPR system has made it possible to precisely edit complex genomic loci such as lncRNAs. Thus, we summarized the advances in CRISPR-Cas approaches for functional studies of lncRNAs including gene knockout, knockdown, overexpression and RNA targeting in tumorigenesis and drug resistance. Additionally, we highlighted the perspectives and potential applications of CRISPR approaches to treat cancer, as an emerging and promising target therapy.
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Affiliation(s)
- Cristiana Libardi Miranda Furtado
- University of Fortaleza, Experimental Biology Center, Fortaleza, Ceara, Brazil.
- Drug Research and Development Center, Postgraduate Program in Translational Medicine, Federal University of Ceara, Fortaleza, Brazil.
| | - Renan da Silva Santos
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceara, Fortaleza, Brazil
| | - Sarah Leyenne Alves Sales
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceara, Fortaleza, Brazil
| | | | - Claudia do Ó Pessoa
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceara, Fortaleza, Brazil
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2
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Zhang Y, Wang S. The possible role of long non-coding RNAs in recurrent miscarriage. Mol Biol Rep 2022; 49:9687-9697. [PMID: 35397764 PMCID: PMC9515028 DOI: 10.1007/s11033-022-07427-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/24/2022] [Indexed: 12/16/2022]
Abstract
Recurrent miscarriage (RM) is a complicated disease in reproductive medicine that impacts many families. Currently, the etiology of RM is thought to include chromosome abnormalities, reproductive tract malformations, autoimmune dysfunction, infection, and environmental factors. However, the underlying mechanisms of RM remain unknown. At present, research on long non-coding RNAs (lncRNAs) is rapidly emerging and becoming a hot research topic in epigenetic studies. Recent studies revealed that lncRNAs are strongly linked to RM and play a crucial role in epigenetic, cell cycle, cell differentiation regulation, and other life activities. This article mainly reviews the difference in lncRNA expression in patients with RM and regulation of susceptibility, endometrial receptivity, and the maternal-fetal interface. Meanwhile, the correlation between lncRNAs and RM is expounded, which provides new insights for the early diagnosis and treatment of RM.
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Affiliation(s)
- Yanan Zhang
- Shandong Key Laboratory of Reproductive Medicine, Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to, Shandong First Medical University, 324 Jingwu Road, Jinan, 250021, China
| | - Shan Wang
- Shandong Key Laboratory of Reproductive Medicine, Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to, Shandong First Medical University, 324 Jingwu Road, Jinan, 250021, China.
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital, Shandong University, 324 Jingwu Road, Jinan, 250021, China.
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3
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Lin Z, Ji X, Tian N, Gan Y, Ke L. Mapping Intellectual Structure for the Long Non-Coding RNA in Hepatocellular Carcinoma Development Research. Front Genet 2022; 12:771810. [PMID: 35047004 PMCID: PMC8762053 DOI: 10.3389/fgene.2021.771810] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/22/2021] [Indexed: 01/09/2023] Open
Abstract
Background: Emerging research suggests that long non-coding RNAs (lncRNAs) play an important role in a variety of developmental or physiological processes of hepatocellular carcinoma (HCC). Various differentially expressed lncRNAs have been identified in HCC. Thus, a deeper analysis of recent research concerning lncRNA and HCC development could provide scientists with a valuable reference for future studies. Methods: Related publications were retrieved from the Web of Science Core Collection database. CiteSpace version 5.6.R4 was employed to conduct bibliometric analysis. Several network maps were constructed to evaluate the collaborations between different countries, institutions, authors, journals, and keywords. Results: A total of 2,667 records were initially found from the year of 2010–2020. The annual related publications output had increased dramatically during these years. Although China was the most prolific country in terms of research publication, the United States played a leading role in collaborative network. The Nanjing Medical University was the most productive institute in the field of lncRNAs in HCC development. Gang Chen was the most prolific researcher, while Yang F was the most frequently co-cited author. Oncotarget, Cell, and Oncogene were the most highly co-cited journals. The most recent burst keywords were interaction, database, and pathway. Conclusion: This study provides a comprehensive overview for the field of lncRNAs in HCC development based on bibliometric and visualized methods. The results would provide a reference for scholars focusing on this field.
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Affiliation(s)
- Zhifeng Lin
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Department of Medical Record, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaohui Ji
- Department of Obstetrics and Gynaecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Nana Tian
- Department of Medical Record, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yu Gan
- Department of Medical Record, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Ke
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Department of Medical Record, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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4
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Koç B, Fucile G, Schmucki R, Giroud N, Bergauer T, Hall BJ. Identification of Natural Antisense Transcripts in Mouse Brain and Their Association With Autism Spectrum Disorder Risk Genes. Front Mol Neurosci 2021; 14:624881. [PMID: 33716665 PMCID: PMC7947803 DOI: 10.3389/fnmol.2021.624881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/03/2021] [Indexed: 11/13/2022] Open
Abstract
Genome-wide sequencing technologies have greatly contributed to our understanding of the genetic basis of neurodevelopmental disorders such as autism spectrum disorder (ASD). Interestingly, a number of ASD-related genes express natural antisense transcripts (NATs). In some cases, these NATs have been shown to play a regulatory role in sense strand gene expression and thus contribute to brain function. However, a detailed study examining the transcriptional relationship between ASD-related genes and their NAT partners is lacking. We performed strand-specific, deep RNA sequencing to profile expression of sense and antisense reads with a focus on 100 ASD-related genes in medial prefrontal cortex (mPFC) and striatum across mouse post-natal development (P7, P14, and P56). Using de novo transcriptome assembly, we generated a comprehensive long non-coding RNA (lncRNA) transcriptome. We conducted BLAST analyses to compare the resultant transcripts with the human genome and identified transcripts with high sequence similarity and coverage. We assembled 32861 de novo antisense transcripts mapped to 12182 genes, of which 1018 are annotated by Ensembl as lncRNA. We validated the expression of a subset of selected ASD-related transcripts by PCR, including Syngap1 and Cntnap2. Our analyses revealed that more than 70% (72/100) of the examined ASD-related genes have one or more expressed antisense transcripts, suggesting more ASD-related genes than previously thought could be subject to NAT-mediated regulation in mice. We found that expression levels of antisense contigs were mostly positively correlated with their cognate coding sense strand RNA transcripts across developmental age. A small fraction of the examined transcripts showed brain region specific enrichment, indicating possible circuit-specific roles. Our BLAST analyses identified 110 of 271 ASD-related de novo transcripts with >90% identity to the human genome at >90% coverage. These findings, which include an assembled de novo antisense transcriptome, contribute to the understanding of NAT regulation of ASD-related genes in mice and can guide NAT-mediated gene regulation strategies in preclinical investigations toward the ultimate goal of developing novel therapeutic targets for ASD.
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Affiliation(s)
- Baran Koç
- Faculty of Science, University of Basel, Basel, Switzerland.,Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.,Neuroscience Discovery, Roche Innovation Center Basel, Basel, Switzerland
| | - Geoffrey Fucile
- sciCORE Computing Center, University of Basel, Basel, Switzerland
| | - Roland Schmucki
- Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.,Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Nicolas Giroud
- Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.,Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Tobias Bergauer
- Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.,Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Benjamin J Hall
- Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.,Neuroscience Discovery, Roche Innovation Center Basel, Basel, Switzerland
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5
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Liu H, Li T, Zhong S, Yu M, Huang W. Intestinal epithelial cells related lncRNA and mRNA expression profiles in dextran sulphate sodium-induced colitis. J Cell Mol Med 2021; 25:1060-1073. [PMID: 33300279 PMCID: PMC7812259 DOI: 10.1111/jcmm.16174] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/10/2020] [Accepted: 11/22/2020] [Indexed: 12/15/2022] Open
Abstract
Intestinal epithelial barrier damage caused by intestinal epithelial cells (IECs) dysfunction plays a crucial role in the pathogenesis and development of inflammatory bowel disease (IBD). Recently, some studies have suggested the emerging role of long non-coding RNAs (lncRNAs) in IBD. The aim of this study was to reveal lncRNAs and mRNA expression profiles in IECs from a mouse model of colitis and to expand our understanding in the intestinal epithelial barrier regulation. IECs from the colons of wild-type mice and dextran sulphate sodium (DSS)-induced mice were isolated for high-throughput RNA-sequencing. A total of 254 up-regulated and 1013 down-regulated mRNAs and 542 up-regulated and 766 down-regulated lncRNAs were detected in the DSS group compared with the Control group. Four mRNAs and six lncRNAs were validated by real-time quantitative PCR. Function analysis showed that dysregulated mRNAs participated in TLR7 signalling pathway, IL-1 receptor activity, BMP receptor binding and IL-17 signalling pathway. Furthermore, the possibility of indirect interactions between differentially expressed mRNAs and lncRNAs was illustrated by the competing endogenous RNA (ceRNA) network. LncRNA ENSMUST00000128026 was predicted to bind to mmu-miR-6899-3p, regulating Dnmbp expression. LncRNA NONMMUT143162.1 was predicted to competitively bind to mmu-miR-6899-3p, regulating Tnip3 expression. Finally, the protein-protein interaction (PPI) network analysis was constructed with 311 nodes and 563 edges. And the highest connectivity degrees were Mmp9, Fpr2 and Ccl3. These results provide novel insights into the functions of lncRNAs and mRNAs involved in the regulation of the intestinal epithelial barrier.
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Affiliation(s)
- Huan Liu
- The Precision Medicine InstituteThe Third Affiliated HospitalSouthern Medical UniversityGuangzhouChina
- Affiliated Traditional Chinese Medicine HospitalSouthwest Medical UniversityLuzhouChina
| | - Teming Li
- Department of General SurgeryXinqiao HospitalArmy Medical UniversityChongqingChina
| | - Shizhen Zhong
- Guangdong Engineering Research Center for Translation of Medical 3D Printing ApplicationGuangdong Provincial Key Laboratory of Medical BiomechanicsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
| | - Min Yu
- Department of General SurgeryXinqiao HospitalArmy Medical UniversityChongqingChina
| | - Wenhua Huang
- The Precision Medicine InstituteThe Third Affiliated HospitalSouthern Medical UniversityGuangzhouChina
- Guangdong Engineering Research Center for Translation of Medical 3D Printing ApplicationGuangdong Provincial Key Laboratory of Medical BiomechanicsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
- Pathological Diagnosis and Research CenterAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
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6
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Nandwani A, Rathore S, Datta M. LncRNAs in cancer: Regulatory and therapeutic implications. Cancer Lett 2020; 501:162-171. [PMID: 33359709 DOI: 10.1016/j.canlet.2020.11.048] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) comprise a class of RNAs that do not code for proteins but are critical in regulating diverse cellular processes and maintaining cell function. In doing so, they have, in recent years, added a potentially new and significant layer of biological regulation. These are more than 200 nucleotides in length and are implicated in a range of diseases and therefore have emerged as potential tools for possible therapeutic intervention. For a disease as complex as cancer, emerging technologies suggest the presence of mutations on genomic loci that do not encode proteins, but give rise to lncRNAs. Aberrant signatures of lncRNAs are now a consistent feature of almost all types of cancers and their associated complications. Analysis and characterisation of functional pathways that lncRNAs are involved with suggest that lncRNAs interact with the chromatin, the protein or with the RNA to demonstrate their cellular effects to modulate proliferation, migration, differentiation, apoptosis and cell death. This review summarizes the current knowledge of lncRNAs, their implications in diverse types of cancer and their possible therapeutic utility.
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Affiliation(s)
- Arun Nandwani
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, India and Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Shalu Rathore
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, India and Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Malabika Datta
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, India and Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
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7
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Shi Z, Ning G, Zhang B, Yuan S, Zhou H, Pan B, Li J, Wei Z, Cao F, Kong X, Feng S. Signatures of altered long noncoding RNAs and messenger RNAs expression in the early acute phase of spinal cord injury. J Cell Physiol 2018; 234:8918-8927. [PMID: 30341912 DOI: 10.1002/jcp.27560] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/14/2018] [Indexed: 12/14/2022]
Abstract
Spinal cord injury (SCI) is a highly severe disease and it can lead to the destruction of the motor and sensory function resulting in temporary or permanent disability. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nt that play a critical role in central nervous system (CNS) injury. However, the exact roles of lncRNAs and messenger RNAs (mRNAs) in the early acute phase of SCI remain to be elucidated. We examined the expression of mRNAs and lncRNAs in a rat model at 2 days after SCI and identified the differentially expressed lncRNAs (DE lncRNAs) and differentially expressed mRNAs (DE mRNAs) using microarray analysis. Subsequently, a comprehensive bioinformatics analysis was also performed to clarify the interaction between DE mRNAs. A total of 3,193 DE lncRNAs and 4,308 DE mRNAs were identified between the injured group and control group. Classification, length distribution, and chromosomal distribution of the dysregulated lncRNAs were also performed. The gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed to identify the critical biological processes and pathways. A protein-protein interaction (PPI) network indicated that IL6, TOP2A, CDK1, POLE, CCNB1, TNF, CCNA2, CDC20, ITGAM, and MYC were the top 10 core genes. The subnetworks from the PPI network were identified to further elucidate the most significant functional modules of the DE mRNAs. These data may provide novel insights into the molecular mechanism of the early acute phase of SCI. The identification of lncRNAs and mRNAs may offer potential diagnostic and therapeutic targets for SCI.
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Affiliation(s)
- Zhongju Shi
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, China.,Department of Neurology, Boston Children's Hospital, F.M. Kirby Neurobiology Center, Harvard Medical School, Boston, Massachusetts
| | - Guangzhi Ning
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Bin Zhang
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Shiyang Yuan
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Hengxing Zhou
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Bin Pan
- Department of Orthopaedics, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jiahe Li
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhijian Wei
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Fujiang Cao
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaohong Kong
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, China
| | - Shiqing Feng
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, China
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8
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Zhou H, Shi Z, Kang Y, Wang Y, Lu L, Pan B, Liu J, Li X, Liu L, Wei Z, Kong X, Feng S. Investigation of candidate long noncoding RNAs and messenger RNAs in the immediate phase of spinal cord injury based on gene expression profiles. Gene 2018; 661:119-125. [PMID: 29580899 DOI: 10.1016/j.gene.2018.03.074] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 03/08/2018] [Accepted: 03/22/2018] [Indexed: 12/23/2022]
Abstract
Spinal cord injury (SCI) is a serious devastating condition and it has a high mortality rate and morbidity rate. The early pathological changes in the immediate phase of SCI may play a major part in the development of secondary injury. Alterations in the expression of many long noncoding RNAs (lncRNAs) have been shown to play fundamental roles in the diseases of the central nervous system. However, the roles of lncRNAs and messenger RNAs (mRNAs) in the immediate phase of SCI are not clear. We examined the expression of mRNAs and lncRNAs in a rat model at 2 h after SCI and identified the differentially expressed lncRNAs (DE lncRNAs) and differentially expressed mRNAs (DE mRNAs) using microarray analysis. 772 DE lncRNAs and 992 DE mRNAs were identified in spinal cord samples in the immediate phase following SCI compared with control samples. Moreover, Gene Ontology (GO) term annotation results showed that CXCR chemokine receptor binding, neutrophil apoptotic process, neutrophil migration, neutrophil extravasation, macrophage differentiation, monocyte chemotaxis and cellular response to interleukin-1 (IL-1) were the main significantly enriched GO terms. The results of Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the DEGs were enriched in toll-like receptor signaling pathway, p53 signaling pathway, MAPK signaling pathway and Jak-STAT signaling pathway. IL6, MBOAT4, FOS, TNF, JUN, STAT3, CSF2, MYC, CCL2 and FGF2 were the top 10 high-degree hub nodes and may be important targets in the immediate phase of SCI. The current study on provides novel insights into how lncRNAs and mRNAs regulate the pathogenesis of the immediate phase after SCI.
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Affiliation(s)
- Hengxing Zhou
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Zhongju Shi
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Yi Kang
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Yao Wang
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Lu Lu
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Bin Pan
- Department of Orthopaedics, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, PR China
| | - Jun Liu
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Xueying Li
- Key Laboratory of Immuno Microenvironment and Disease of the Educational Ministry of China, Department of Immunology, Tianjin Medical University, Tianjin, PR China
| | - Lu Liu
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Zhijian Wei
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Xiaohong Kong
- 221 Laboratory, School of Medicine, Nankai University, Tianjin, PR China.
| | - Shiqing Feng
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, PR China.
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9
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Wang Q, Jiang S, Song A, Hou S, Wu Q, Qi L, Gao X. HOXD-AS1 functions as an oncogenic ceRNA to promote NSCLC cell progression by sequestering miR-147a. Onco Targets Ther 2017; 10:4753-4763. [PMID: 29033588 PMCID: PMC5628688 DOI: 10.2147/ott.s143787] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is one of the most common malignancies worldwide, and it occurs at a higher frequency in males. HOXD-AS1, an important cancer-associated long noncoding RNA (lncRNA), contributes to the development and progression of several cancers. However, the exact roles of HOXD-AS1 in NSCLC progression are still unknown. Here, we investigated the underlying mechanisms of HOXD-AS1 in human NSCLC tissues. We found that lncRNA HOXD-AS1 was specifically upregulated (P<0.001) in NSCLC tissues and promoted cancer cell growth by targeting miR-147a. Moreover, HOXD-AS1 expression positively correlated with NSCLC clinical pathologic characteristics (tumor size, P=0.006; tumor stage, P=0.044; recurrence, P=0.031) and survival rate (P=0.003). HOXD-AS1 knockdown reduced proliferation and promoted apoptosis of NSCLC cells. The dual-luciferase reporter assay showed that HOXD-AS1 could negatively regulate the expression of miR-147a. miR-147a inhibition abrogated the effect of HOXD-AS1 knockdown on the proliferation and apoptosis of NSCLC cells. Furthermore, HOXD-AS1 positively regulated the expression of pRB (a tumor suppressor protein) in NSCLC cells. Taken together, our data indicated that HOXD-AS1 might be an oncogenic lncRNA that promotes proliferation of NSCLC and could be a therapeutic target in NSCLC.
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Affiliation(s)
- Qinghua Wang
- State Key Laboratory of Pharmaceutical Biotechnology.,MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing.,Laboratory Animal Center, Nantong University
| | - Shujun Jiang
- State Key Laboratory of Pharmaceutical Biotechnology.,MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing
| | - Anying Song
- State Key Laboratory of Pharmaceutical Biotechnology.,MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing
| | - Siyuan Hou
- State Key Laboratory of Pharmaceutical Biotechnology.,MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing
| | - Qinfeng Wu
- Department of Rehabilitation, Affiliated Hospital of Nantong University, Nantong University
| | - Longju Qi
- Interventional Therapy Department of the Third People's Hospital of Nantong City, Nantong University, Nantong, People's Republic of China
| | - Xiang Gao
- State Key Laboratory of Pharmaceutical Biotechnology.,MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing
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10
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Lu C, Ma J, Cai D. Increased HAGLR expression promotes non-small cell lung cancer proliferation and invasion via enhanced de novo lipogenesis. Tumour Biol 2017; 39:1010428317697574. [PMID: 28443464 DOI: 10.1177/1010428317697574] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Lung cancers are broadly classified into small cell lung cancer and non-small cell lung cancer, with non-small cell lung cancer one of the leading causes of cancer-associated deaths worldwide. Presently, the mechanisms underlying lung tumorigenesis remain incompletely understood. Accumulating evidence indicates that abnormal expression of long non-coding RNAs is associated with tumorigenesis in multiple cancers, including lung cancer. HAGLR messenger RNA of non-small cell lung cancer tissues was significantly higher. Moreover, high levels of HAGLR expression were associated with non-small cell lung cancer tumor lymph node metastasis status, stage, and poor overall survival. Inhibition of HAGLR in non-small cell lung cancer cells suppressed cell proliferation and invasion. RNA interference-mediated downregulation of HAGLR also decreased levels of fatty acid synthase, with fatty acid synthase levels positively correlated with HAGLR expression in non-small cell lung cancer specimens. In addition, the cellular free fatty acid content of cancer cells was decreased following HAGLR knockdown. HAGLR depletion significantly inhibited the growth of non-small cell lung cancer cells in vivo. Furthermore, the expression levels of p21 and matrix metallopeptidase-9 (MMP-9) were dysregulated when HAGLR expression was suppressed. Our results suggest that HAGLR is an important regulator of non-small cell lung cancer cell proliferation and invasion, perhaps by regulating fatty acid synthase. Therefore, targeting HAGLR may be a possible therapeutic strategy for non-small cell lung cancer.
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Affiliation(s)
- Chunwei Lu
- Department of Integrated Traditional Chinese and Western Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jun Ma
- Department of Integrated Traditional Chinese and Western Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dingfang Cai
- Department of Integrated Traditional Chinese and Western Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
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11
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Huang F, Yi J, Zhou T, Gong X, Jiang H, Yao X. Toward Understanding Non-coding RNA Roles in Intracranial Aneurysms and Subarachnoid Hemorrhage. Transl Neurosci 2017; 8:54-64. [PMID: 28729919 PMCID: PMC5516590 DOI: 10.1515/tnsci-2017-0010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 04/25/2017] [Indexed: 12/11/2022] Open
Abstract
Subarachnoid hemorrhage (SAH) is a common and frequently life-threatening cerebrovascular disease, which is mostly related with a ruptured intracranial aneurysm. Its complications include rebleeding, early brain injury, cerebral vasospasm, delayed cerebral ischemia, chronic hydrocephalus, and also non neurological problems. Non-coding RNAs (ncRNAs), comprising of microRNAs (miRNAs), small interfering RNAs (siRNAs) and long non-coding RNAs (lncRNAs), play an important role in intracranial aneurysms and SAH. Here, we review the non-coding RNAs expression profile and their related mechanisms in intracranial aneurysms and SAH. Moreover, we suggest that these non-coding RNAs function as novel molecular biomarkers to predict intracranial aneurysms and SAH, and may yield new therapies after SAH in the future.
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Affiliation(s)
- Fengzhen Huang
- Department of Neurology, the First People's Hospital of Chenzhou, Chenzhou, Hunan, 423000, P. R.China
| | - Jiping Yi
- Department of Neurology, the First People's Hospital of Chenzhou, Chenzhou, Hunan, 423000, P. R.China
| | - Tieqiao Zhou
- Department of Laboratory Medicine, the First People's Hospital of Chenzhou, Chenzhou, Hunan, 423000, P. R.China
| | - Xiaoxiang Gong
- Pediatrics, the Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011 P. R.China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R.China.,State Key Laboratory of Medical Genetics of China, Central South University, Changsha, Hunan, 410078, P. R.China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, 410008, P. R.China
| | - Xiaoxi Yao
- Department of Neurology, the First People's Hospital of Chenzhou, Chenzhou, Hunan, 423000, P. R.China
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12
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Amirkhah R, Farazmand A, Wolkenhauer O, Schmitz U. RNA Systems Biology for Cancer: From Diagnosis to Therapy. Methods Mol Biol 2016; 1386:305-30. [PMID: 26677189 DOI: 10.1007/978-1-4939-3283-2_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
It is due to the advances in high-throughput omics data generation that RNA species have re-entered the focus of biomedical research. International collaborate efforts, like the ENCODE and GENCODE projects, have spawned thousands of previously unknown functional non-coding RNAs (ncRNAs) with various but primarily regulatory roles. Many of these are linked to the emergence and progression of human diseases. In particular, interdisciplinary studies integrating bioinformatics, systems biology, and biotechnological approaches have successfully characterized the role of ncRNAs in different human cancers. These efforts led to the identification of a new tool-kit for cancer diagnosis, monitoring, and treatment, which is now starting to enter and impact on clinical practice. This chapter is to elaborate on the state of the art in RNA systems biology, including a review and perspective on clinical applications toward an integrative RNA systems medicine approach. The focus is on the role of ncRNAs in cancer.
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Affiliation(s)
- Raheleh Amirkhah
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Ali Farazmand
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
| | - Ulf Schmitz
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.
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Transcriptomic Profiling Discloses Molecular and Cellular Events Related to Neuronal Differentiation in SH-SY5Y Neuroblastoma Cells. Cell Mol Neurobiol 2016; 37:665-682. [PMID: 27422411 DOI: 10.1007/s10571-016-0403-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/09/2016] [Indexed: 12/21/2022]
Abstract
Human SH-SY5Y neuroblastoma cells are widely utilized in in vitro studies to dissect out pathogenetic mechanisms of neurodegenerative disorders. These cells are considered as neuronal precursors and differentiate into more mature neuronal phenotypes under selected growth conditions. In this study, in order to decipher the pathways and cellular processes underlying neuroblastoma cell differentiation in vitro, we performed systematic transcriptomic (RNA-seq) and bioinformatic analysis of SH-SY5Y cells differentiated according to a two-step paradigm: retinoic acid treatment followed by enriched neurobasal medium. Categorization of 1989 differentially expressed genes (DEGs) identified in differentiated cells functionally linked them to changes in cell morphology including remodelling of plasma membrane and cytoskeleton, and neuritogenesis. Seventy-three DEGs were assigned to axonal guidance signalling pathway, and the expression of selected gene products such as neurotrophin receptors, the functionally related SLITRK6, and semaphorins, was validated by immunoblotting. Along with these findings, the differentiated cells exhibited an ability to elongate longer axonal process as assessed by the neuronal cytoskeletal markers biochemical characterization and morphometric evaluation. Recognition of molecular events occurring in differentiated SH-SY5Y cells is critical to accurately interpret the cellular responses to specific stimuli in studies on disease pathogenesis.
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Li J, Zhuang C, Liu Y, Chen M, Chen Y, Chen Z, He A, Lin J, Zhan Y, Liu L, Xu W, Zhao G, Guo Y, Wu H, Cai Z, Huang W. Synthetic tetracycline-controllable shRNA targeting long non-coding RNA HOXD-AS1 inhibits the progression of bladder cancer. J Exp Clin Cancer Res 2016; 35:99. [PMID: 27328915 PMCID: PMC4915162 DOI: 10.1186/s13046-016-0372-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/08/2016] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have been proved to act as key molecules in cancer development and progression. Dysregulation of lncRNAs is discovered in various tumor tissues and cancer cells where they can serve as oncogenes or tumor suppressors. Long non-coding RNA HOXD-AS (HOXD cluster antisense RNA 1) has recently been identified to be involved in the development of several cancers including neuroblastoma, adenocarcinomas and breast cancer. However, the role of HOXD-AS1 in bladder cancer remains unknown. METHODS The synthetic tetracycline-controllable shRNA was used to modulate the level of HOXD-AS1 by adding different concentrations of doxycycline (dox). RT-qPCR was used to detect the expression level of HOXD-AS1. Cell proliferation was determined by CCK-8 assay and EdU incorporation experiment when HOXD-AS1 was knocked down. We used wound-healing assay for detecting the effect of HOXD-AS1 on cell migration. Eventually, cell apoptosis was determined by caspase 3 ELISA assay and flow cytometry assay. RESULTS In this study, we found that the expression level of HOXD-AS1 was significantly increased in bladder cancer tissues and cells. Furthermore, high expression of HOXD-AS1 was significantly related to tumor size, histological grade and TNM stage. In vitro assays confirmed that knockdown of HOXD-AS1 suppressed cell proliferation/migration and increased the rate of apoptotic cell in bladder cancer cells. At last, we used the important element of synthetic biology, tetracycline(tet)-controllable switch, to construct tet-controllable shRNA vectors which can modulate the expression of HOXD-AS1 in a dosage-dependent manner. CONCLUSIONS Our research suggested that high expression of HOXD-AS1 may be involved in the bladder cancer carcinogenesis through inhibiting the phenotypes and activating endogenous cancer-related molecular pathways. Therefore, HOXD-AS1 may act as an oncogene and provide a potential attractive therapeutic target for bladder cancer. In addition, the synthetic tetracycline-controllable shRNA may provide a novel method for cancer research in vitro assays.
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Affiliation(s)
- Jianfa Li
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Shantou University Medical College, First Affiliated Hospital of Shenzhen University, Shenzhen, 518039, Guangdong Province, People's Republic of China
- Shantou University Medical College, Shantou, 515041, Guangdong Province, People's Republic of China
| | - Chengle Zhuang
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Shantou University Medical College, First Affiliated Hospital of Shenzhen University, Shenzhen, 518039, Guangdong Province, People's Republic of China
- Shantou University Medical College, Shantou, 515041, Guangdong Province, People's Republic of China
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, 518036, People's Republic of China
| | - Yuchen Liu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Shantou University Medical College, First Affiliated Hospital of Shenzhen University, Shenzhen, 518039, Guangdong Province, People's Republic of China
| | - Mingwei Chen
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Shantou University Medical College, First Affiliated Hospital of Shenzhen University, Shenzhen, 518039, Guangdong Province, People's Republic of China
- Anhui Medical University, Hefei, 230000, Anhui Province, People's Republic of China
| | - Yincong Chen
- Shantou University Medical College, Shantou, 515041, Guangdong Province, People's Republic of China
| | - Zhicong Chen
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Shantou University Medical College, First Affiliated Hospital of Shenzhen University, Shenzhen, 518039, Guangdong Province, People's Republic of China
- Shantou University Medical College, Shantou, 515041, Guangdong Province, People's Republic of China
| | - Anbang He
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Shantou University Medical College, First Affiliated Hospital of Shenzhen University, Shenzhen, 518039, Guangdong Province, People's Republic of China
- Anhui Medical University, Hefei, 230000, Anhui Province, People's Republic of China
| | - Junhao Lin
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Shantou University Medical College, First Affiliated Hospital of Shenzhen University, Shenzhen, 518039, Guangdong Province, People's Republic of China
- Shantou University Medical College, Shantou, 515041, Guangdong Province, People's Republic of China
| | - Yonghao Zhan
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Shantou University Medical College, First Affiliated Hospital of Shenzhen University, Shenzhen, 518039, Guangdong Province, People's Republic of China
- Shantou University Medical College, Shantou, 515041, Guangdong Province, People's Republic of China
| | - Li Liu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Shantou University Medical College, First Affiliated Hospital of Shenzhen University, Shenzhen, 518039, Guangdong Province, People's Republic of China
- Shantou University Medical College, Shantou, 515041, Guangdong Province, People's Republic of China
| | - Wen Xu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Shantou University Medical College, First Affiliated Hospital of Shenzhen University, Shenzhen, 518039, Guangdong Province, People's Republic of China
| | - Guoping Zhao
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Centerat Shanghai, Shanghai, 200000, People's Republic of China
| | - Yinglu Guo
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing, 100034, People's Republic of China
| | - Hanwei Wu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Shantou University Medical College, First Affiliated Hospital of Shenzhen University, Shenzhen, 518039, Guangdong Province, People's Republic of China
| | - Zhiming Cai
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Shantou University Medical College, First Affiliated Hospital of Shenzhen University, Shenzhen, 518039, Guangdong Province, People's Republic of China.
- Shantou University Medical College, Shantou, 515041, Guangdong Province, People's Republic of China.
- Anhui Medical University, Hefei, 230000, Anhui Province, People's Republic of China.
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing, 100034, People's Republic of China.
| | - Weiren Huang
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Shantou University Medical College, First Affiliated Hospital of Shenzhen University, Shenzhen, 518039, Guangdong Province, People's Republic of China.
- Shantou University Medical College, Shantou, 515041, Guangdong Province, People's Republic of China.
- Anhui Medical University, Hefei, 230000, Anhui Province, People's Republic of China.
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing, 100034, People's Republic of China.
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Qiu H, Liu Q, Li J, Wang X, Wang Y, Yuan Z, Li J, Pei DS. Analysis of the association of HOTAIR single nucleotide polymorphism (rs920778) and risk of cervical cancer. APMIS 2016; 124:567-73. [PMID: 27229487 DOI: 10.1111/apm.12550] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/08/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Haifeng Qiu
- Department of Obstetrics and Gynecology; The First Affiliated Hospital of Zhengzhou University; Zhengzhou China
- Ovarian and Cervical Disease Clinical Treatment Center of Henan Province; The First Affiliated Hospital of Zhengzhou University; Zhengzhou China
| | - Qiuli Liu
- Department of Gynecologic Oncology; The Affiliated Hospital of Jiangnan University and The Fourth People's Hospital of Wuxi; Wuxi China
| | - Juan Li
- School of Medicine; Jiangsu University; Zhenjiang China
| | - Xiujuan Wang
- Department of Obstetrics and Gynecology; The First Affiliated Hospital of Zhengzhou University; Zhengzhou China
- Ovarian and Cervical Disease Clinical Treatment Center of Henan Province; The First Affiliated Hospital of Zhengzhou University; Zhengzhou China
| | - Yuan Wang
- Department of Gynecologic Oncology; The Affiliated Hospital of Jiangnan University and The Fourth People's Hospital of Wuxi; Wuxi China
| | - Zhongfu Yuan
- Department of Obstetrics and Gynecology; The First Affiliated Hospital of Zhengzhou University; Zhengzhou China
- Ovarian and Cervical Disease Clinical Treatment Center of Henan Province; The First Affiliated Hospital of Zhengzhou University; Zhengzhou China
| | - Jing Li
- Department of Oncology; The First Affiliated Hospital of Zhengzhou University; Zhengzhou China
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16
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Lin S, Zhang L, Luo W, Zhang X. Characteristics of Antisense Transcript Promoters and the Regulation of Their Activity. Int J Mol Sci 2015; 17:E9. [PMID: 26703594 PMCID: PMC4730256 DOI: 10.3390/ijms17010009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/23/2015] [Accepted: 12/16/2015] [Indexed: 02/07/2023] Open
Abstract
Recently, an increasing number of studies on natural antisense transcripts have been reported, especially regarding their classification, temporal and spatial expression patterns, regulatory functions and mechanisms. It is well established that natural antisense transcripts are produced from the strand opposite to the strand encoding a protein. Despite the pivotal roles of natural antisense transcripts in regulating the expression of target genes, the transcriptional mechanisms initiated by antisense promoters (ASPs) remain unknown. To date, nearly all of the studies conducted on this topic have focused on the ASP of a single gene of interest, whereas no study has systematically analyzed the locations of ASPs in the genome, ASP activity, or factors influencing this activity. This review focuses on elaborating on and summarizing the characteristics of ASPs to extend our knowledge about the mechanisms of antisense transcript initiation.
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Affiliation(s)
- Shudai Lin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
| | - Li Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
- Agricultural College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
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Tao H, Yang JJ, Zhou X, Deng ZY, Shi KH, Li J. Emerging role of long noncoding RNAs in lung cancer: Current status and future prospects. Respir Med 2015; 110:12-9. [PMID: 26603340 DOI: 10.1016/j.rmed.2015.10.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 01/01/2023]
Abstract
Lung cancer is the leading cause of cancer-related death worldwide with a 5-year survival rate of less than 15%, despite significant advances in both diagnostic and therapeutic approaches. Combined genomic and transcriptomic sequencing studies have identified numerous genetic driver mutations that are responsible for the development of lung cancer. Importantly, these approaches have also uncovered the widespread expression of "noncoding RNAs" including long noncoding RNAs (LncRNAs), which impact biologic responses through the regulation of mRNA transcription or translation. To date, most studies of the role of noncoding RNAs have focused on LncRNAs, which regulate mRNA translation via the RNA interference pathway. Although many of their attributes, such as patterns of expression, remain largely unknown, LncRNAs have key functions in transcriptional, post-transcriptional, and epigenetic gene regulation. Recent research showed that LncRNAs regulate flowering time in the lung cancer. In this review, we discuss these investigations into long noncoding RNAs were performed almost exclusively in lung cancer. Future work will need to extend these into lung cancer and to analyze how LncRNAs interact to regulate mRNA expression. From a clinical perspective, the targeting of LncRNAs as a novel therapeutic approach will require a deeper understanding of their function and mechanism of action.
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Affiliation(s)
- Hui Tao
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei 230601, China
| | - Jing-Jing Yang
- Department of Pharmacology, The Second Hospital of Anhui Medical University, Hefei 230601, China
| | - Xiao Zhou
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei 230601, China.
| | - Zi-Yu Deng
- Department of Scientific and Educational, The Second Hospital of Anhui Medical University, China
| | - Kai-Hu Shi
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei 230601, China.
| | - Jun Li
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
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Yarmishyn AA, Batagov AO, Tan JZ, Sundaram GM, Sampath P, Kuznetsov VA, Kurochkin IV. HOXD-AS1 is a novel lncRNA encoded in HOXD cluster and a marker of neuroblastoma progression revealed via integrative analysis of noncoding transcriptome. BMC Genomics 2014; 15 Suppl 9:S7. [PMID: 25522241 PMCID: PMC4290621 DOI: 10.1186/1471-2164-15-s9-s7] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Long noncoding RNAs (lncRNAs) constitute a major, but poorly characterized part of human transcriptome. Recent evidence indicates that many lncRNAs are involved in cancer and can be used as predictive and prognostic biomarkers. Significant fraction of lncRNAs is represented on widely used microarray platforms, however they have usually been ignored in cancer studies. Results We developed a computational pipeline to annotate lncRNAs on popular Affymetrix U133 microarrays, creating a resource allowing measurement of expression of 1581 lncRNAs. This resource can be utilized to interrogate existing microarray datasets for various lncRNA studies. We found that these lncRNAs fall into three distinct classes according to their statistical distribution by length. Remarkably, these three classes of lncRNAs were co-localized with protein coding genes exhibiting distinct gene ontology groups. This annotation was applied to microarray analysis which identified a 159 lncRNA signature that discriminates between localized and metastatic stages of neuroblastoma. Analysis of an independent patient cohort revealed that this signature differentiates also relapsing from non-relapsing primary tumors. This is the first example of the signature developed via the analysis of expression of lncRNAs solely. One of these lncRNAs, termed HOXD-AS1, is encoded in HOXD cluster. HOXD-AS1 is evolutionary conserved among hominids and has all bona fide features of a gene. Studying retinoid acid (RA) response of SH-SY5Y cell line, a model of human metastatic neuroblastoma, we found that HOXD-AS1 is a subject to morphogenic regulation, is activated by PI3K/Akt pathway and itself is involved in control of RA-induced cell differentiation. Knock-down experiments revealed that HOXD-AS1 controls expression levels of clinically significant protein-coding genes involved in angiogenesis and inflammation, the hallmarks of metastatic cancer. Conclusions Our findings greatly extend the number of noncoding RNAs functionally implicated in tumor development and patient treatment and highlight their role as potential prognostic biomarkers of neuroblastomas.
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Esguerra JLS, Eliasson L. Functional implications of long non-coding RNAs in the pancreatic islets of Langerhans. Front Genet 2014; 5:209. [PMID: 25071836 PMCID: PMC4083688 DOI: 10.3389/fgene.2014.00209] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/19/2014] [Indexed: 12/14/2022] Open
Abstract
Type-2 diabetes (T2D) is a complex disease characterized by insulin resistance in target tissues and impaired insulin release from pancreatic beta cells. As central tissue of glucose homeostasis, the pancreatic islet continues to be an important focus of research to understand the pathophysiology of the disease. The increased access to human pancreatic islets has resulted in improved knowledge of islet function, and together with advances in RNA sequencing and related technologies, revealed the transcriptional and epigenetic landscape of human islet cells. The discovery of thousands of long non-coding RNA (lncRNA) transcripts highly enriched in the pancreatic islet and/or specifically expressed in the beta-cells, points to yet another layer of gene regulation of many hitherto unknown mechanistic principles governing islet cell functions. Here we review fundamental islet physiology and propose functional implications of the lncRNAs in islet development and endocrine cell functions. We also take into account important differences between rodent and human islets in terms of morphology and function, and suggest how species-specific lncRNAs may partly influence gene regulation to define the unique phenotypic identity of an organism and the functions of its constituent cells. The implication of primate-specific lncRNAs will be far-reaching in all aspects of diabetes research, but most importantly in the identification and development of novel targets to improve pancreatic islet cell functions as a therapeutic approach to treat T2D.
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Affiliation(s)
- Jonathan L S Esguerra
- Islet Cell Exocytosis, Department of Clinical Sciences-Malmö, Lund University Diabetes Centre, Lund University Malmö, Sweden
| | - Lena Eliasson
- Islet Cell Exocytosis, Department of Clinical Sciences-Malmö, Lund University Diabetes Centre, Lund University Malmö, Sweden
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Khorkova O, Myers AJ, Hsiao J, Wahlestedt C. Natural antisense transcripts. Hum Mol Genet 2014; 23:R54-63. [PMID: 24838284 DOI: 10.1093/hmg/ddu207] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Recent years have seen the increasing understanding of the crucial role of RNA in the functioning of the eukaryotic genome. These discoveries, fueled by the achievements of the FANTOM, and later GENCODE and ENCODE consortia, led to the recognition of the important regulatory roles of natural antisense transcripts (NATs) arising from what was previously thought to be 'junk DNA'. Roughly defined as non-coding regulatory RNA transcribed from the opposite strand of a coding gene locus, NATs are proving to be a heterogeneous group with high potential for therapeutic application. Here, we attempt to summarize the rapidly growing knowledge about this important non-coding RNA subclass.
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Affiliation(s)
- Olga Khorkova
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | | | - Jane Hsiao
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - Claes Wahlestedt
- Department of Psychiatry and Behavioral Sciences and Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami, FL 33136, USA
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Bhan A, Mandal SS. Long noncoding RNAs: emerging stars in gene regulation, epigenetics and human disease. ChemMedChem 2014; 9:1932-56. [PMID: 24677606 DOI: 10.1002/cmdc.201300534] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Indexed: 12/19/2022]
Abstract
Noncoding RNAs (ncRNAs) are classes of transcripts that are encoded by the genome and transcribed but never get translated into proteins. Though not translated into proteins, ncRNAs play pivotal roles in a variety of cellular functions. Here, we review the functions of long noncoding RNAs (lncRNAs) and their implications in various human diseases. Increasing numbers of studies demonstrate that lncRNAs play critical roles in regulation of protein-coding genes, maintenance of genomic integrity, dosage compensation, genomic imprinting, mRNA processing, cell differentiation, and development. Misregulation of lncRNAs is associated with a variety of human diseases, including cancer, immune and neurological disorders. Different classes of lncRNAs, their functions, mechanisms of action, and associations with different human diseases are summarized in detail, highlighting their as yet untapped potential in therapy.
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Affiliation(s)
- Arunoday Bhan
- Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019 (USA)
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Schönbach C, Shen B, Tan T, Ranganathan S. InCoB2013 introduces Systems Biology as a major conference theme. BMC SYSTEMS BIOLOGY 2013; 7 Suppl 3:S1. [PMID: 24555777 PMCID: PMC3816296 DOI: 10.1186/1752-0509-7-s3-s1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The Asia-Pacific Bioinformatics Network (APBioNet) held the first International Conference on Bioinformatics (InCoB) in Bangkok in 2002 to promote North-South networking. Commencing as a forum for Asia-Pacific researchers to interact with and learn from with scientists of developed countries, InCoB has become a major regional bioinformatics conference, with participants from the region as well as North America and Europe. Since 2006, InCoB has selected the best submissions for publication in BMC Bioinformatics. In response to the growth and maturation of data-driven approaches, InCoB added BMC Genomics in 2009 and with the introduction of this conference supplement, BMC Systems Biology to its journal choices for submitting authors. Co-hosting InCoB2013 with the second International Conference for Translational Bioinformatics (ICTBI) is in line with InCoB's support for the current trend in taking bioinformatics to the bedside, along with a systems approach to solving biological problems.
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